"We are displeased with the holding of the conference and the activities of the associations that organised it and we are exercising our democratic right to demonstrate our displeasure," one of the organisers said.
Dozens of protesters rallied outside the hotel, carrying placards with the names of Croatian towns that were damaged during the 1991-1995 war and with messages against the conference and the International Criminal Tribunal for the former Yugoslavia (ICTY).
The protest was scheduled to end by noon.
The two-day conference was organised by the Zagreb-based Documenta Centre for Confrontation with the Past, the Humanitarian Law Fund from Belgrade and the Research and Documentation Centre from Sarajevo.
The meeting will be addressed, among others, by Croatian President Stjepan Mesic, ICTY President Fausto Pocar, ICTY Chief Prosecutor Carla del Ponte, Croatian Deputy Prime Minister Jadranka Kosor and Chief Public Prosecutor Mladen Bajic.